Quantitative Analysis of Adenosine-to-Inosine RNA Editing

Malik, Turnee N; Cartailler, Jean‐Philippe; Emeson, Ronald B.

doi:10.1007/978-1-0716-0787-9_7

Cited by 9 publications

(3 citation statements)

References 18 publications

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“…PCR was also conducted without RT to confirm the absence of any amplification of residual plasmid DNA. The quantification of editing at the amber/W site was conducted by determining the percentage of edited residues in the amber/W site through analysis of sequencing chromatograms (C/T in the genomic sequence) ( An et al., 2019 ; Hsu et al., 2019 ; Malik et al., 2021 ). The primers used for assessing the editing of HDV-1 clone I were the same as previously described ( Hsu et al., 2019 ).…”

Section: Methodsmentioning

confidence: 99%

Unbranched rod-like RNA is required for RNA editing of hepatitis delta virus genotype 2 and genotype 4

Hsu,

Chen

et al. 2023

Virus Research

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Section: Methodsmentioning

confidence: 99%

Unbranched rod-like RNA is required for RNA editing of hepatitis delta virus genotype 2 and genotype 4

Hsu,

Chen

et al. 2023

Virus Research

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“…Purified PCR amplicons were sequenced using the reverse primer indicated above. Relative peak heights in sequence electropherogram traces were used to quantify RNA editing, as previously described (Malik et al., 2021).…”

Section: Methodsmentioning

confidence: 99%

RNA editing‐mediated regulation of calcium‐dependent activator protein for secretion (CAPS1) localization and its impact on synaptic transmission

Shumate

Tas

Kavalali

et al. 2021

Journal of Neurochemistry

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Calcium-dependent activator protein for secretion 1 (CAPS1) is a SNARE accessory protein that facilitates formation of the SNARE complex to enable neurotransmitter release. Messenger RNAs encoding CAPS1 are subject to a site-specific adenosineto-inosine (A-to-I) editing event resulting in a glutamate-to-glycine (E-to-G) substitution in the C-terminal domain of the encoded protein product. The C-terminal domain of CAPS1 is necessary for its synaptic enrichment and Cadps RNA editing has been shown previously to enhance the release of neuromodulatory transmitters. Using mutant mouse lines engineered to solely express CAPS1 protein isoforms encoded by either the non-edited or edited Cadps transcript, primary neuronal cultures from mouse hippocampus were used to explore the effect of Cadps editing on neurotransmission and CAPS1 synaptic localization at both glutamatergic and GABAergic synapses. While the editing of Cadps does not alter baseline evoked neurotransmission, it enhances short-term synaptic plasticity, specifically short-term depression, at inhibitory synapses. Cadps editing also alters spontaneous inhibitory neurotransmission. Neurons that solely express edited Cadps have a greater proportion of synapses that contain CAPS1 than neurons that solely express non-edited Cadps for both glutamatergic and GABAergic synapses. Editing of Cadps transcripts is regulated by neuronal activity, as global network stimulation increases the extent of transcripts edited in wild-type hippocampal neurons, whereas chronic network silencing decreases the level of Cadps editing. Taken together, these results provide key insights into the importance of Cadps editing in modulating its own synaptic localization, as well as the modulation of neurotransmission at inhibitory synapses in hippocampal neurons.

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“…The edited inosine base pairs with cytidine in cDNA, hence editing is visible as an A-to-G sequence change. Recently, sophisticated bioinformatics tools have been developed to maximize detection accuracy, while minimizing the detection of false positives [ 145 , 146 ]. Furthermore, considerable effort has been made to comprehensively detect and remove known SNPs from editing datasets and databases [ 147 , 148 ].…”

Section: Detection Of Modified Nucleotidesmentioning

confidence: 99%

Long Non-Coding RNA Epigenetics

Kazimierczyk

Wrzesiński

2021

IJMS

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Long noncoding RNAs exceeding a length of 200 nucleotides play an important role in ensuring cell functions and proper organism development by interacting with cellular compounds such as miRNA, mRNA, DNA and proteins. However, there is an additional level of lncRNA regulation, called lncRNA epigenetics, in gene expression control. In this review, we describe the most common modified nucleosides found in lncRNA, 6-methyladenosine, 5-methylcytidine, pseudouridine and inosine. The biosynthetic pathways of these nucleosides modified by the writer, eraser and reader enzymes are important to understanding these processes. The characteristics of the individual methylases, pseudouridine synthases and adenine–inosine editing enzymes and the methods of lncRNA epigenetics for the detection of modified nucleosides, as well as the advantages and disadvantages of these methods, are discussed in detail. The final sections are devoted to the role of modifications in the most abundant lncRNAs and their functions in pathogenic processes.

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Quantitative Analysis of Adenosine-to-Inosine RNA Editing

Cited by 9 publications

References 18 publications

Unbranched rod-like RNA is required for RNA editing of hepatitis delta virus genotype 2 and genotype 4

Unbranched rod-like RNA is required for RNA editing of hepatitis delta virus genotype 2 and genotype 4

RNA editing‐mediated regulation of calcium‐dependent activator protein for secretion (CAPS1) localization and its impact on synaptic transmission

Long Non-Coding RNA Epigenetics

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